Last seen, apparently being poisoned in "In a Mirror, Darkly", it probably turns out he was merely drugged because Hoshi Sato needed him alive for some other purpose, for a Season 5 sequel to that story. Archer eventually escapes her clutches, finds the unstable interphase area of space through which the U.S.S. Defiant arrived - thinking he could use it to go steal more future tech to bring back and overthrow the Empress - only to go in and end up stranded in the Prime Universe's 28th Century instead. Still obsessed with how historically important his other self is by comparison to his career, and unable to get back, he schemes to use temporal communication equipment to destablize that 22nd Century and undermine the NX-01's missions as described in the Defiant's logs. By the time he figures out how to acquire the ability to time-travel, divided and full of untrustworthy, aggressive aliens everywhere - it'll be an easier place to conquer and create a new Terran Empire in.